6Z4T | pdb_00006z4t

sperm whale myoglobin mutant (H64V V64A) bearing the non-canonical amino acid 2-Amino-3-(thiazol-5-yl)propanoic acid as axial heme ligand


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.23 Å
  • R-Value Free: 
    0.188 (Depositor), 0.187 (DCC) 
  • R-Value Work: 
    0.150 (Depositor), 0.151 (DCC) 
  • R-Value Observed: 
    0.152 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 3.0 of the entry. See complete history

Literature

Noncanonical Heme Ligands Steer Carbene Transfer Reactivity in an Artificial Metalloenzyme*.

Pott, M.Tinzl, M.Hayashi, T.Ota, Y.Dunkelmann, D.Mittl, P.R.E.Hilvert, D.

(2021) Angew Chem Int Ed Engl 60: 15063-15068

  • DOI: https://doi.org/10.1002/anie.202103437
  • Primary Citation Related Structures: 
    6Z4R, 6Z4T

  • PubMed Abstract: 

    Changing the primary metal coordination sphere is a powerful strategy for tuning metalloprotein properties. Here we used amber stop codon suppression with engineered pyrrolysyl-tRNA synthetases, including two newly evolved enzymes, to replace the proximal histidine in myoglobin with N δ -methylhistidine, 5-thiazoylalanine, 4-thiazoylalanine and 3-(3-thienyl)alanine. In addition to tuning the heme redox potential over a >200 mV range, these noncanonical ligands modulate the protein's carbene transfer activity with ethyl diazoacetate. Variants with increased reduction potential proved superior for cyclopropanation and N-H insertion, whereas variants with reduced E o values gave higher S-H insertion activity. Given the functional importance of histidine in many enzymes, these genetically encoded analogues could be valuable tools for probing mechanism and enabling new chemistries.


  • Organizational Affiliation
    • Laboratory of Organic Chemistry, ETH Zürich, 8093, Zürich, Switzerland.

Macromolecule Content 

  • Total Structure Weight: 17.89 kDa 
  • Atom Count: 1,518 
  • Modeled Residue Count: 154 
  • Deposited Residue Count: 154 
  • Unique protein chains: 1

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Myoglobin154Physeter macrocephalusMutation(s): 3 
Gene Names: MB
EC: 1.11.1 (UniProt), 1.7 (UniProt)
UniProt
Find proteins for P02185 (Physeter macrocephalus)
Explore P02185 
Go to UniProtKB:  P02185
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP02185
Sequence Annotations
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Reference Sequence

Small Molecules

Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
Q75
Query on Q75
A
L-PEPTIDE LINKINGC6 H8 N2 O2 SHIS

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.23 Å
  • R-Value Free:  0.188 (Depositor), 0.187 (DCC) 
  • R-Value Work:  0.150 (Depositor), 0.151 (DCC) 
  • R-Value Observed: 0.152 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 40.009α = 90
b = 47.327β = 90
c = 76.897γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
PHENIXmodel building
PHENIXphasing
PHENIXrefinement

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-04-28
    Type: Initial release
  • Version 1.1: 2021-06-30
    Changes: Database references
  • Version 2.0: 2023-09-13
    Changes: Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Polymer sequence, Structure summary
  • Version 2.1: 2024-01-24
    Changes: Refinement description
  • Version 3.0: 2025-07-30
    Changes: Polymer sequence, Structure summary